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Ryan Peek
I have worked in many rivers and aquatic systems in California, and continue to strive to find ways to apply research to conservation management. I am particularly interested in using a confluence of disciplines such as genomics, hydrology, ecology, and geomorphology to better understand current and future impacts to our freshwater ecosystems.
I am a strong advocate for open science, and education; and giving voices, training, and space for folks who support and foster a supportive community with diverse questions and views.
Education
PhD, Ecology (with certificate in Conservation Management)
UC Davis
Davis, CA
2018 - 2014
- Population genetics of a sentinel stream-breeding frog (Rana boylii)
M.S., Biology
University of San Francisco
San Francisco, CA
2010 - 2008
- Thesis: Landscape Genetics of Foothill Yellow-Legged Frogs (Rana boylii) in regulated and unregulated rivers: Assessing connectivity and genetic fragmentation
B.S. Wildlife, Fish & Conservation Ecology
UC Davis
Davis, CA
2002 - 1998
- Emphasis in Behavioral Ecology
Research Experience
Post-doctoral Researcher
Center for Watershed Sciences
UC Davis
2020 - 2018
- Analysis of connectivity and genetic health of rare endemic frogs in CA, NV, and AZ to inform conservation management.
- Analysis of floodplain foodwebs for salmon to better understand connectivity and seasonality for management.
- Research and analysis on how to link ecological bioassessment data with flow management for functional environmental flows.
Graduate Student Researcher
Center for Watershed Sciences
UC Davis
2018 - 2014
- Research in amphibian/aquatic ecology, with particular focus on assessing ecological health with molecular techniques to inform conservation in river ecosystems.
Jr. Research Specialist
Center for Watershed Sciences
UC Davis
2014 - 2011
- Research in stream ecology and montane aquatic ecosystems, with particular focus on ecosystem function and hydroclimatic impacts on regulated rivers in the Sierra Nevada.
Biological Science Technician
USDA Forest Service, Pacific Southwest Research Station
Davis, CA
2010
- Developed and designed website on ecology, river regulation and conservation of the foothill yellow-legged frog (Rana boylii), including GIS synthesis and development of a distribution map showing over 6,000 records from multiple sources (http://gis.fs.fed.us/psw/topics/wildlife/herp/rana_boylii/).
- Conducted 1-D RHABSIM modeling and analysis. Coordinate field research, data collection, and writing.
Research Assistant II
UC Berkeley
Berkeley, CA
2010 - 2009
- As part of a California Energy Commission study of regulated flow effects on foothill yellow-legged frog (Rana boylii) breeding habitat, led field research crews for extensive field data collection.
- Collaborated with Sarah Yarnell and Amy Lind on field methodology and integrating graduate research with the grant research.
Research Assistant II
UC Davis
Davis, CA
2009
- Working with Sarah Kupferberg and Alessandro Catenazzi, assisted in research, as part of a California Energy Commission study, of regulated flow effects on water temperatures and foothill yellow-legged frog (Rana boylii)
- Including predation experiments and tadpole growth experiments, Helped deploy thermographs in various Sierran rivers throughout California. Conducting research on tributary density in relation to amphibian occupancy in regulated rivers in California.
Industry Experience
I have worked in a variety of places including the National Park Service, US Forest Service, environmental consulting, and even a glass fabrication plant. I appreciate supportive and collaborative communities.
Fish & Wildlife Biologist
Stillwater Sciences
Davis CA
2011 - 2002
- Field and Project Manager, conducted research in aquatic, terrestrial, and riparian ecosystems. Assisted in the development of restoration, conservation, and management strategies in various watersheds throughout California and Oregon for amphibian and fisheries related projects.
- Extensive experience completing watershed analyses. Successfully worked independently and collaboratively on various projects including leading field crews, managing budgets, conducting meetings, analyzing data, and writing comprehensive reports.
- Watershed Experience: Alameda Creek (San Francisco Public Utilities Commission), Upper American River (Sacramento Municipal Utility District), South Fork Feather River (South Feather Water & Power), Yuba River (North, Middle, and South) (CH2MHill), Napa River and Floodplain (US Army Corp of Engineers), Santa Clara River (California State Coastal Conservancy), McKenzie River (Eugene Water and Electric Board), Upper Merced River (Merced Alliance), Butte Creek and West Branch Feather River (PG&E), McCloud and Pit Rivers (PG&E)
Biological Science Technician
National Park Service
Sequoia & Kings Canyon, CA
2001
- Part of a 2-person backcountry crew working on a federally threatened Sierra/Mountain yellow-legged frog (Rana sierrae) conservation and restoration project during the initial year of the project.
- This position involved extensive backpacking and hiking experience while living in remote and rugged terrain at 10,000-12,000 feet for multiple weeks at a time. Required the ability to work independently, efficiently, and safely.
- Conducted amphibian surveys of mountain lakes and identified amphibian species in larval and adult stages, habitat assessment, data collection, and non-native fish removal.
Teaching Experience
I am passionate about education, and strive to continue learning how to be a better teacher. I am a proud Carpentries Instructor, and the community they represent.
Strategies & Techniques for Analyzing Microbial Population Structures
Marine Biological Laboratory
Woods Hole, MA
2020 - 2019
- Research facilitator/teacher for the STAMPS course on analysis of metagenomic data. Provided interdisciplinary bioinformatic and statistical training to practitioners of molecular microbial ecology and genomics.
- Topics covered included acquisition and organization of next generation sequence data; principles of quality control of sequence data and data management; methods of taxonomic assignment and clustering of targeted gene data. Also an introduction to the Linux command-line and R statistical environments. (https://www.mbl.edu/education/courses/stamps/)
R for Data Analysis and Visualization in Science
UC Davis
Davis, CA
2019 - 2017
- Lead instructor and creator of graduate course teaching R and version control for 25+ students. Course designed to train students in toolsets applicable to the entire process of reproducible data-driven research and encourage the use of open-source tools.
- Built website and made course materials openly available on github. (https://gge-ucd.github.io/R-DAVIS/).
- now a required graduate course in Ecology
Foothill Yellow-Legged Frog Ecology, Management, and Regulation
Humboldt State
Arcata, CA
2018
- One of three main instructors for workshop designed to cover the natural history and management of the foothill yellow-legged frog.
- Three days of lecture followed by a field day covered ecological requirements of the species, mitigation, restoration, and permitting requirements if listing takes place
Intro to Genomics (Data Carpentry)
DIBSI
Davis, CA
2018
- Co-instructor. Data Intensive Biology Summer Institute at UC Davis is a series of two-day or week-long workshops for biologists to learn bioinformatics and data science. The Intro to R course was built as an interactive, week-long introduction to the programming language R. Following Carpentry workshop content, taught basics of R by live-coding with participants
- (https://dib-lab.github.io/2018-06-27-DIBSI-Genomics/)
Intro to R
DIBSI
Davis, CA
2017
- Co-Instructor. Data Intensive Biology Summer Institute at UC Davis is a series of two-day or week-long workshops for biologists to learn bioinformatics and data science. The Intro to R course was built as an interactive, week-long introduction to the programming language R. Following Carpentry workshop content, taught basics of R by live-coding with participants
- (https://mikoontz.github.io/data-carpentry-week/)
Ecogeomorphology
UC Davis
Davis, CA
2015
- Co-instructor. Taught advanced undergraduate students to multidisciplinary collaborative watershed and stream analysis through combined laboratory and field study of a selected stream system. Educated students from diverse backgrounds to work in interdisciplinary research teams to collect and analyze field data from the Tuolumne River system.
- Serve as rafting guide, as well as lectured, and taught in classroom, lab, and field, including a 3 day rafting trip on the Tuolumne River. (https://watershed.ucdavis.edu/education/classes/)
Geospatial Analysis
University of San Francisco
San Francisco, CA
2010
- Teaching Assistant
- Lab instructor for undergraduate geospatial analysis course using ArcGIS; planned and conducted lab activities and led discussions for one semester
Data Carpentry Workshops
Various
N/A
202 - 2016
- Teach researchers in science, engineering, medicine, and related disciplines the computing skills they need to get more done using open source and reproducible tools. Specifically, have taught genomics/ecology/geospatial workshops at Stanford, UC Davis, UC Berkeley, and University of Rhode Island Coastal Institute. (http://software-carpentry.org/) (http://www.datacarpentry.org/)
Selected Data Science Writing
I like writing stuff about data science, R, making maps, and frogs ryanpeek.org
Using AWK and R to Parse 25tb
LiveFreeOrDichotomize.com
N/A
2019
- Story of parsing large amounts of genomics data.
- Provided advice for dealing with data much larger than disk.
- Reached top of HackerNews.
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Selected Press (About)
Great paper? Swipe right on the new ‘Tinder for preprints’ app
Science
N/A
2017
- Story of the app Papr made with Jeff Leek and Lucy D’Agostino McGowan.
Swipe right for science: Papr app is ‘Tinder for preprints’
Nature News
N/A
2017
- Second press article for app Papr.
The Deeper Story in the Data
University of Vermont Quarterly
N/A
2016
- Story on my path post graduation and the power of narrative.
Selected Press (By)
The Great Student Migration
The New York Times
N/A
2016
- Most shared and discussed article from the New York Times for August 2016.
Wildfires are Getting Worse, The New York Times
The New York Times
N/A
2016
- GIS analysis and modeling of fire patterns and trends
- Data in collaboration with NASA and USGS
Who’s Speaking at the Democratic National Convention?
The New York Times
N/A
2016
- Data scraped from CSPAN records to figure out who talked and past conventions.
Who’s Speaking at the Republican National Convention?
The New York Times
N/A
2016
- Used same data scraping techniques as Who’s Speaking at the Democratic National Convention?
A Trail of Terror in Nice, Block by Block
The New York Times
N/A
2016
- Led research effort to put together story of 2016 terrorist attack in Nice, France in less than 12 hours.
- Work won Silver medal at Malofiej 2017, and gold at Society of News and Design.
Selected Publications, Posters, and Talks
Charge Reductions Associated with Shortening Time to Recovery in Septic Shock
Chest
N/A
2019
- Authored with Wesley H. Self, MD MPH; Dandan Liu, PhD; Stephan Russ, MD, MPH; Michael J. Ward, MD, PhD, MBA; Nathan I. Shapiro, MD, MPH; Todd W. Rice, MD, MSc; Matthew W. Semler, MD, MSc.
Multimorbidity Explorer | A shiny app for exploring EHR and biobank data
RStudio::conf 2019
N/A
2019
- Contributed Poster. Authored with Yaomin Xu.
Taking a network view of EHR and Biobank data to find explainable multivariate patterns
Vanderbilt Biostatistics Seminar Series
N/A
2019
- University wide seminar series.
R timelineViz: Visualizing the distribution of study events in longitudinal studies
Under-Review (copy available upon request.)
N/A
2018
- Authored with Alex Sunderman of the Vanderbilt Department of Epidemiology.
Asymmetric Linkage Disequilibrium: Tools for Dissecting Multiallelic LD
Journal of Human Immunology
N/A
2015
- Authored with Richard Single, Vanja Paunic, Mark Albrecht, and Martin Maiers.
An Agent Based Model of Mysis Migration
International Association of Great Lakes Research Conference
N/A
2015
- Authored with Brian O’Malley, Sture Hansson, and Jason Stockwell.